Roey Angel 2021-02-20
Here we attempt to detect ASVs that were labelled with 13C in our soil incubations using differential abundance modelling. Using DESeq2 (Love, Huber and Anders 2014) we compare the relative abundance of each ASV in the fractions where 13C-labelled RNA is expected to be found (>1.795 g ml-1; AKA ‘heavy’ fractions) to the fractions where unlabelled RNA is expected to be found (<1.795 g ml-1; AKA ‘light’ fractions). The method has been previously described in Angel et al., (2018).
set.seed(2021)
alpha_thresh <- 0.05
LFC_thresh <- 0.26
samples_prep_path <- "./"
data_path <- "./DADA2_pseudo/"
# Metadata_table <- "./AnCUE_Metadata_decontam.csv"
# Seq_table <- "DADA2.seqtab_nochim_decontam.tsv"
# Seq_file <- "DADA2.Seqs_decontam.fa"
Ps_file <- "Ps_obj_decontam_filt3.Rds"
Tree_file <- "./Tree/DADA2.Seqs_decontam_filtered.filtered.align.treefile"# Load phylogenetic tree
Tree <- read_tree(paste0(data_path, Tree_file))
# load and merge phyloseq object
readRDS(paste0(data_path, Ps_file)) %>%
merge_phyloseq(.,
phy_tree(Tree)
) -> Ps_obj_SIP## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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Because the DESeq2 models will be run on each gradient separately, we
need to subset This is easily done using
HTSSIP::phyloseq_subset (Youngblut, Barnett and Buckley
2018)
# split, ignore time points (for labelled ASV plots)
test_expr_1 <- "(Site == '${Site}' & Oxygen == '${Oxygen}' & Label..13C. == 'Unlabelled') | (Site == '${Site}' & Oxygen == '${Oxygen}' & Label..13C. == '${Label..13C.}')"
params_1 <- get_treatment_params(Ps_obj_SIP, c("Site",
"Oxygen",
"Glucose",
"Label..13C."),
"Label..13C. != 'Unlabelled'")## Warning: `filter_()` was deprecated in dplyr 0.7.0.
## Please use `filter()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Ps_obj_SIP_noTime_l <- phyloseq_subset(Ps_obj_SIP, params_1, test_expr_1) ## Warning: `mutate_()` was deprecated in dplyr 0.7.0.
## Please use `mutate()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
# names(Ps_obj_SIP_noTime_l) %<>%
# map(., ~str_remove_all(.x, "\\s\\|\\s.*")) %>%
# map(., ~str_remove_all(.x, "\\(|\\)|Site == |Hours == |Oxygen == |Label..13C. == |'")) %>%
# map(., ~str_replace_all(.x, "([0-9]+)", "\\1 h"))
# split, include time points (for DESeq2 modelling)
test_expr_2 <- "(Site == '${Site}' & Hours == '${Hours}' & Oxygen == '${Oxygen}' & Label..13C. == '${Label..13C.}') | (Site == '${Site}' & Hours == '${Hours}' & Oxygen == '${Oxygen}' & Label..13C. == '${Label..13C.}')"
params_2 <- get_treatment_params(Ps_obj_SIP, c("Site",
"Hours",
"Oxygen",
"Glucose",
"Label..13C."))
# Generate a list of subsetted phyloseq objects
Ps_obj_SIP_byTime_l <- phyloseq_subset(Ps_obj_SIP, params_2, test_expr_2)
names(Ps_obj_SIP_byTime_l) %<>%
map(., ~str_remove_all(.x, "\\s\\|\\s.*")) %>%
map(., ~str_remove_all(.x, "\\(|\\)|Site == |Hours == |Oxygen == |Label..13C. == |'")) %>%
map(., ~str_replace_all(.x, "([0-9]+)", "\\1 h")) Let us look first at the dissimilarity in community composition between the different fractions. If the labelling was strong enough we should see a deivation of (some of) the heavy fractions from the light ones. However, a lack of a significant deviation does not mean unsuccesful labelling because if only a small minority of the community was labelled we might not see it here (but we will, hopefully, see it using DESeq2 modelling).
(mod1 <- adonis2(vegdist(otu_table(Ps_obj_SIP), method = "horn") ~ Site * Oxygen * Hours + Lib.size,
data = as(sample_data(Ps_obj_SIP), "data.frame"),
permutations = 999
))| Df | SumOfSqs | R2 | F | Pr(\>F) | |
|---|---|---|---|---|---|
| Site | 1 | 27.4431088 | 0.5392110 | 480.477524 | 0.001 |
| Oxygen | 1 | 5.2895923 | 0.1039316 | 92.610872 | 0.001 |
| Hours | 1 | 0.1596437 | 0.0031367 | 2.795063 | 0.054 |
| Lib.size | 1 | 0.0777490 | 0.0015276 | 1.361239 | 0.244 |
| Site:Oxygen | 1 | 0.5404132 | 0.0106182 | 9.461624 | 0.001 |
| Site:Hours | 1 | 0.4190994 | 0.0082346 | 7.337646 | 0.003 |
| Oxygen:Hours | 1 | 0.1185437 | 0.0023292 | 2.075479 | 0.116 |
| Site:Oxygen:Hours | 1 | 0.2259389 | 0.0044393 | 3.955768 | 0.021 |
| Residual | 291 | 16.6208496 | 0.3265718 | NA | NA |
| Total | 299 | 50.8949386 | 1.0000000 | NA | NA |
plot_lib_dist(Ps_obj_SIP)## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Ps_obj_SIP %>%
scale_libraries(round = "round") ->
Ps_obj_SIP_scaled## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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plot_lib_dist(Ps_obj_SIP_scaled)## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
(mod2 <- adonis2(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn") ~ Site * Oxygen * Hours + Lib.size,
data = as(sample_data(Ps_obj_SIP_scaled), "data.frame"),
permutations = 999
))| Df | SumOfSqs | R2 | F | Pr(\>F) | |
|---|---|---|---|---|---|
| Site | 1 | 27.6580326 | 0.5391944 | 482.574243 | 0.001 |
| Oxygen | 1 | 5.3811011 | 0.1049048 | 93.888847 | 0.001 |
| Hours | 1 | 0.1610764 | 0.0031402 | 2.810443 | 0.054 |
| Lib.size | 1 | 0.0690842 | 0.0013468 | 1.205374 | 0.304 |
| Site:Oxygen | 1 | 0.5817234 | 0.0113407 | 10.149844 | 0.001 |
| Site:Hours | 1 | 0.4264653 | 0.0083140 | 7.440919 | 0.001 |
| Oxygen:Hours | 1 | 0.1115178 | 0.0021740 | 1.945750 | 0.139 |
| Site:Oxygen:Hours | 1 | 0.2278696 | 0.0044423 | 3.975843 | 0.021 |
| Residual | 291 | 16.6782367 | 0.3251428 | NA | NA |
| Total | 299 | 51.2951071 | 1.0000000 | NA | NA |
(mod3 <- adonis2(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn") ~ Site * Oxygen * Hours * Density.zone,
data = as(sample_data(Ps_obj_SIP_scaled), "data.frame"),
permutations = 999
))| Df | SumOfSqs | R2 | F | Pr(\>F) | |
|---|---|---|---|---|---|
| Site | 1 | 27.6580326 | 0.5391944 | 710.3918641 | 0.001 |
| Oxygen | 1 | 5.3811011 | 0.1049048 | 138.2126674 | 0.001 |
| Hours | 1 | 0.1610764 | 0.0031402 | 4.1372204 | 0.026 |
| Density.zone | 2 | 2.4171422 | 0.0471223 | 31.0419431 | 0.001 |
| Site:Oxygen | 1 | 0.5264587 | 0.0102633 | 13.5220022 | 0.001 |
| Site:Hours | 1 | 0.4072149 | 0.0079387 | 10.4592446 | 0.001 |
| Oxygen:Hours | 1 | 0.0884712 | 0.0017247 | 2.2723677 | 0.105 |
| Site:Density.zone | 1 | 0.1749105 | 0.0034099 | 4.4925470 | 0.010 |
| Oxygen:Density.zone | 1 | 2.7697312 | 0.0539960 | 71.1400749 | 0.001 |
| Hours:Density.zone | 1 | 0.0296273 | 0.0005776 | 0.7609713 | 0.493 |
| Site:Oxygen:Hours | 1 | 0.1426365 | 0.0027807 | 3.6635948 | 0.027 |
| Site:Oxygen:Density.zone | 1 | 0.0681521 | 0.0013286 | 1.7504743 | 0.185 |
| Site:Hours:Density.zone | 1 | 0.1071922 | 0.0020897 | 2.7532144 | 0.057 |
| Oxygen:Hours:Density.zone | 1 | 0.2601483 | 0.0050716 | 6.6818640 | 0.002 |
| Site:Oxygen:Hours:Density.zone | 1 | 0.0850351 | 0.0016578 | 2.1841127 | 0.134 |
| Residual | 283 | 11.0181769 | 0.2147998 | NA | NA |
| Total | 299 | 51.2951071 | 1.0000000 | NA | NA |
Site_disp <- betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), get_variable(Ps_obj_SIP_scaled, "Site"))## Warning in betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), :
## some squared distances are negative and changed to zero
permutest(Site_disp)##
## Permutation test for homogeneity of multivariate dispersions
## Permutation: free
## Number of permutations: 999
##
## Response: Distances
## Df Sum Sq Mean Sq F N.Perm Pr(>F)
## Groups 1 0.2375 0.237546 5.5678 999 0.016 *
## Residuals 298 12.7139 0.042664
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(Site_disp)Oxygen_disp <- betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), get_variable(Ps_obj_SIP_scaled, "Oxygen"))## Warning in betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), :
## some squared distances are negative and changed to zero
permutest(Oxygen_disp)##
## Permutation test for homogeneity of multivariate dispersions
## Permutation: free
## Number of permutations: 999
##
## Response: Distances
## Df Sum Sq Mean Sq F N.Perm Pr(>F)
## Groups 1 0.03023 0.0302278 3.1681 999 0.087 .
## Residuals 298 2.84331 0.0095413
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(Oxygen_disp)Hours_disp <- betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), get_variable(Ps_obj_SIP_scaled, "Hours"))## Warning in betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), :
## some squared distances are negative and changed to zero
permutest(Hours_disp)##
## Permutation test for homogeneity of multivariate dispersions
## Permutation: free
## Number of permutations: 999
##
## Response: Distances
## Df Sum Sq Mean Sq F N.Perm Pr(>F)
## Groups 4 0.2595 0.064877 4.7232 999 0.002 **
## Residuals 295 4.0520 0.013736
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(Hours_disp)Density_disp <- betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), get_variable(Ps_obj_SIP_scaled, "Density.zone"))## Warning in betadisper(vegdist(otu_table(Ps_obj_SIP_scaled), method = "horn"), :
## some squared distances are negative and changed to zero
permutest(Density_disp)##
## Permutation test for homogeneity of multivariate dispersions
## Permutation: free
## Number of permutations: 999
##
## Response: Distances
## Df Sum Sq Mean Sq F N.Perm Pr(>F)
## Groups 2 0.48515 0.242577 24.876 999 0.001 ***
## Residuals 297 2.89621 0.009752
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
plot(Density_disp)Ord <- ordinate(Ps_obj_SIP_scaled, "CAP", "horn",
formula = ~ Site * Oxygen * Hours * Density.zone)
explained <- as.numeric(format(round(eigenvals(Ord)/sum(eigenvals(Ord)) * 100, 1), nsmall = 1))
Ord_plt <- plot_ordination(Ps_obj_SIP, Ord, type = "samples", color = "Label..13C.", justDF = TRUE)
p_ord_joint <- ggplot(Ord_plt) +
geom_point(aes(
x = CAP1,
y = CAP2,
color = Label..13C.,
size = Density..g.ml.1.,
shape = Oxygen
), alpha = 2 / 3) +
guides(colour = guide_legend(title = "Labelling"),
size = guide_legend(title = "Density (g ml<sup>-1</sup>)"),
shape = guide_legend(title = "Oxygen")) +
scale_colour_locuszoom() +
# scale_colour_manual(values = Gradient.colours) +
# scale_fill_manual(values = Gradient.colours, guide = "none") +
labs(x = sprintf("CAP1 (%s%%)", explained[1]),
y = sprintf("CAP2 (%s%%)", explained[2])) +
coord_fixed(ratio = sqrt(explained[2] / explained[1])) +
theme(legend.justification = "top",
legend.title = element_markdown(size = 11)
) +
scale_size_continuous(breaks = round(c(seq(min(Ord_plt$Density..g.ml.1.),
max(Ord_plt$Density..g.ml.1.),
length.out = 5),
1), 4),
range = c(0.1, 5)) +
facet_grid(Site ~ Hours) +
# ggtitle("Joint analysis") +
NULL
save_figure(paste0(fig.path, "Oridnation"),
p_ord_joint,
pwidth = 10,
pheight = 8,
dpi = 600)## Loading required package: ragg
knitr::include_graphics(paste0(fig.path, "Oridnation", ".png"))Now run the differential abundance models using DESeq2. We then
filter the resutls to include only ASVs with Log_2_ fold change
>LFC_thresh and significant at
P<alpha_thresh. Lastly, we run ‘LFC-shrinking’ based on
Stephens (2016).
# generate a deseq object
DESeq_obj_SIP_byTime_l <- mclapply(Ps_obj_SIP_byTime_l,
function(x) {phyloseq_to_deseq2_safe(x,
test_condition = "Density.zone",
ref_level = "Light")},
mc.cores = nrow(params_2))
# run dds pipeline
DESeq_obj_SIP_byTime_l %<>% mclapply(.,
function(x) {DESeq(x,
test = "Wald",
fitType = "local")},
mc.cores = nrow(params_2)) # run dds pipeline
# extract results from a DESeq analysis
DESeq_res_SIP_byTime_l <- mclapply(DESeq_obj_SIP_byTime_l,
function(x) {
results(x,
altHypothesis = "greater",
alpha = alpha_thresh,
contrast = c("Density.zone", "Heavy", "Light"))}, # redundant if phyloseq_to_deseq2_safe() was used but doesn't hurt
mc.cores = nrow(params_2))
DESeq_res_SIP_byTime_LFC_l <- mclapply(DESeq_obj_SIP_byTime_l,
function(x) {
results(x,
lfcThreshold = LFC_thresh,
altHypothesis = "greater",
alpha = alpha_thresh,
contrast = c("Density.zone", "Heavy", "Light"))}, # redundant if phyloseq_to_deseq2_safe() was used but doesn't hurt
mc.cores = nrow(params_2)) # Extract results from a DESeq analysis
DESeq_res_SIP_byTime_LFC_shrink_l <- map(seq(length(DESeq_obj_SIP_byTime_l)),
~lfcShrink(DESeq_obj_SIP_byTime_l[[.x]],
res = DESeq_res_SIP_byTime_LFC_l[[.x]],
coef = "Density.zone_Heavy_vs_Light",
type = "ashr"))## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
## Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
## https://doi.org/10.1093/biostatistics/kxw041
names(DESeq_res_SIP_byTime_LFC_shrink_l) <- names(DESeq_res_SIP_byTime_LFC_l)
# Compare
plotMA(DESeq_res_SIP_byTime_l[[2]], ylim = c(-2,2))plotMA(DESeq_res_SIP_byTime_LFC_l[[2]], ylim = c(-2,2))plotMA(DESeq_res_SIP_byTime_LFC_shrink_l[[2]], ylim = c(-2,2))# summarise results (lfcShrink doesn't change the values)
# map2(DESeq_res_SIP_byTime_l, print(names(DESeq_res_SIP_byTime_l)), ~summary(.x)) # summarise results
# for (i in seq(1, length(DESeq_res_SIP_byTime_l))) { # didn't manage with map
# print(names(DESeq_res_SIP_byTime_l[i]))
# summary(DESeq_res_SIP_byTime_l[[i]])
# }
for (i in seq(1, length(DESeq_res_SIP_byTime_LFC_l))) { # didn't manage with map
print(names(DESeq_res_SIP_byTime_LFC_l[i]))
summary(DESeq_res_SIP_byTime_LFC_l[[i]])
}## [1] "Certovo & 12 h & Anoxic & Labelled"
##
## out of 3026 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 0, 0%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 3, 0.099%
## low counts [2] : 7, 0.23%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 216 h & Anoxic & Labelled"
##
## out of 2878 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 37, 1.3%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1484, 52%
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 24 h & Anoxic & Labelled"
##
## out of 2755 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 1, 0.036%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 4, 0.15%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 48 h & Anoxic & Labelled"
##
## out of 2787 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 15, 0.54%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1222, 44%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 216 h & Anoxic & Unlabelled"
##
## out of 2825 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 0, 0%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 5, 0.18%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 12 h & Oxic & Labelled"
##
## out of 3053 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 7, 0.23%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 8, 0.26%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 24 h & Oxic & Labelled"
##
## out of 2954 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 107, 3.6%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 905, 31%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 48 h & Oxic & Labelled"
##
## out of 2882 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 122, 4.2%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 331, 11%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 72 h & Oxic & Labelled"
##
## out of 2898 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 142, 4.9%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 1, 0.035%
## low counts [2] : 1329, 46%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Certovo & 72 h & Oxic & Unlabelled"
##
## out of 2979 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 33, 1.1%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 4, 0.13%
## low counts [2] : 1995, 67%
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 12 h & Anoxic & Labelled"
##
## out of 3031 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 27, 0.89%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1678, 55%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 216 h & Anoxic & Labelled"
##
## out of 3210 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 0, 0%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 116, 3.6%
## low counts [2] : 3, 0.093%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 24 h & Anoxic & Labelled"
##
## out of 2848 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 22, 0.77%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 2340, 82%
## (mean count < 15)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 48 h & Anoxic & Labelled"
##
## out of 2758 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 12, 0.44%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1527, 55%
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 216 h & Anoxic & Unlabelled"
##
## out of 2862 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 0, 0%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 2, 0.07%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 12 h & Oxic & Labelled"
##
## out of 2923 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 57, 2%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 1, 0.034%
## low counts [2] : 1790, 61%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 24 h & Oxic & Labelled"
##
## out of 2548 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 101, 4%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1061, 42%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 48 h & Oxic & Labelled"
##
## out of 2531 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 13, 0.51%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1820, 72%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 72 h & Oxic & Labelled"
##
## out of 2556 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 115, 4.5%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 0, 0%
## low counts [2] : 1113, 44%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
##
## [1] "Plesne & 72 h & Oxic & Unlabelled"
##
## out of 2798 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.26 (up) : 3, 0.11%
## LFC < -0.26 (down) : 0, 0%
## outliers [1] : 7, 0.25%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
# Store labelled ASVs and save them to a file
# DESeq_res_SIP_byTime_l %>%
# map(., ~subset(.x, padj < alpha_thresh & log2FoldChange > LFC_thresh)) %>%
# map(., ~as.data.frame(.x)) %>%
# map(., ~rownames_to_column(.x, "ASV")) %>%
# bind_rows(., .id = "Comparison") %>%
# arrange(Comparison, desc(baseMean)) %T>%
# write_csv(., file = "DESeq2_byTime_a-0.05.txt") ->
# DESeq_res_SIP_byTime_df
# Store labelled ASVs and save them to a file
DESeq_res_SIP_byTime_LFC_shrink_l %>%
map(., ~subset(.x, padj < alpha_thresh & log2FoldChange > LFC_thresh)) %>%
map(., ~as.data.frame(.x)) %>%
map(., ~rownames_to_column(.x, "ASV")) %>%
bind_rows(., .id = "Comparison") %>%
arrange(Comparison, desc(baseMean)) %>%
separate(., "Comparison" ,c("Site","Hours", "Oxygen", "Label"), sep = " & ") ->
DESeq_res_SIP_byTime_LFC_sig_df
# grab the taxonomy of the ASVs
prune_taxa(DESeq_res_SIP_byTime_LFC_sig_df$ASV, Ps_obj_SIP) %>%
tax_table() %>%
as("data.frame") %>%
rownames_to_column("ASV") %>%
merge(., DESeq_res_SIP_byTime_LFC_sig_df, by = "ASV") %>% # watch out: this merge recycles values!
arrange(Site, Oxygen, Hours, baseMean) %>%
write_csv(., file = "DESeq2_byTime_a-0.05_LFC0-322.txt")## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
DESeq_res_SIP_byTime_LFC_sig_df %>%
get_variable() %>%
select_if(is.numeric) %>%
vis_value()## Warning: `gather_()` was deprecated in tidyr 1.2.0.
## Please use `gather()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
DESeq_res_SIP_byTime_LFC_sig_df %>%
get_variable() %>%
select_if(is.numeric) %>%
vis_cor()# DESeq_results <- DESeq_res_SIP_byTime_LFC_shrink_l[2]
# plot_DESeq(DESeq_results, Ps_obj_SIP, plot_title = names(DESeq_results))
DESeq_plots <- map(seq(length(DESeq_res_SIP_byTime_LFC_shrink_l)),
~plot_DESeq(DESeq_res_SIP_byTime_LFC_shrink_l[.x],
Ps_obj_SIP, plot_title = names(DESeq_res_SIP_byTime_LFC_shrink_l[.x])))## Loading required package: ggrepel
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Note: Using an external vector in selections is ambiguous.
## ℹ Use `all_of(rank)` instead of `rank` to silence this message.
## ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
##
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
##
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
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## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in speedyseq::psmelt(ps_obj_glom_rel): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
Certovo_DESeq <- ((DESeq_plots[[6]] +
theme(legend.position = "none") +
theme(axis.text.x = element_blank())) +
(DESeq_plots[[1]] +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank())) +
(DESeq_plots[[7]] +
theme(legend.position = "none",
axis.text.x = element_blank())) +
(DESeq_plots[[3]] +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank())) +
(DESeq_plots[[8]] +
theme(legend.position = "none") +
theme(legend.position = "none",
axis.text.x = element_blank())) +
(DESeq_plots[[4]] +
theme(legend.position = "none") +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank()) +
ylim(NA, 5)) +
(DESeq_plots[[9]] +
theme(legend.position = "none",
axis.text.x = element_blank())) +
(DESeq_plots[[2]] +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank())) +
(DESeq_plots[[10]] +
theme(legend.position = "none") +
ylim(NA, 5)) +
(DESeq_plots[[5]] +
theme(legend.position = "none",
axis.title.y = element_blank())) +
plot_layout(ncol = 2, guides = "collect") &
theme(legend.position = 'bottom'))
save_figure(paste0(fig.path, "Certovo_DESeq2"),
Certovo_DESeq,
pwidth = 8,
pheight = 10,
dpi = 600)## Warning: Removed 3046 rows containing missing values (geom_segment).
## Warning: Removed 3026 rows containing missing values (geom_segment).
## Warning: Removed 2862 rows containing missing values (geom_segment).
## Warning: Removed 2755 rows containing missing values (geom_segment).
## Warning: Removed 2775 rows containing missing values (geom_segment).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 2774 rows containing missing values (geom_segment).
## Warning: Removed 2785 rows containing missing values (geom_segment).
## Warning: Removed 2856 rows containing missing values (geom_segment).
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 2969 rows containing missing values (geom_segment).
## Warning: Removed 2825 rows containing missing values (geom_segment).
## Warning: Removed 3046 rows containing missing values (geom_segment).
## Warning: Removed 3026 rows containing missing values (geom_segment).
## Warning: Removed 2862 rows containing missing values (geom_segment).
## Warning: Removed 2755 rows containing missing values (geom_segment).
## Warning: Removed 2775 rows containing missing values (geom_segment).
## Warning: Removed 1 rows containing missing values (geom_point).
## Warning: Removed 2774 rows containing missing values (geom_segment).
## Warning: Removed 2785 rows containing missing values (geom_segment).
## Warning: Removed 2856 rows containing missing values (geom_segment).
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 2969 rows containing missing values (geom_segment).
## Warning: Removed 2825 rows containing missing values (geom_segment).
knitr::include_graphics(paste0(fig.path, "Certovo_DESeq2", ".png"))Plesne_DESeq <- ((DESeq_plots[[16]] +
theme(legend.position = "none") +
theme(axis.text.x = element_blank())) +
(DESeq_plots[[11]] +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank())) +
(DESeq_plots[[17]] +
theme(legend.position = "none",
axis.text.x = element_blank())) +
(DESeq_plots[[13]] +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank())) +
(DESeq_plots[[18]] +
theme(legend.position = "none") +
theme(legend.position = "none",
axis.text.x = element_blank())) +
(DESeq_plots[[14]] +
theme(legend.position = "none") +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank())) +
(DESeq_plots[[19]] +
theme(legend.position = "none",
axis.text.x = element_blank())) +
(DESeq_plots[[12]] +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.title.y = element_blank()) +
ylim(-3, NA)) +
(DESeq_plots[[20]] +
theme(legend.position = "none")) +
(DESeq_plots[[15]] +
theme(legend.position = "none",
axis.title.y = element_blank())) +
plot_layout(ncol = 2, guides = "collect") &
theme(legend.position = 'bottom'))
save_figure(paste0(fig.path, "Plesne_DESeq2"),
Plesne_DESeq,
pwidth = 8,
pheight = 10,
dpi = 600)## Warning: Removed 2867 rows containing missing values (geom_segment).
## Warning: Removed 3012 rows containing missing values (geom_segment).
## Warning: Removed 2463 rows containing missing values (geom_segment).
## Warning: Removed 2841 rows containing missing values (geom_segment).
## Warning: Removed 2518 rows containing missing values (geom_segment).
## Warning: Removed 2746 rows containing missing values (geom_segment).
## Warning: Removed 2460 rows containing missing values (geom_segment).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 3210 rows containing missing values (geom_segment).
## Warning: Removed 2795 rows containing missing values (geom_segment).
## Warning: Removed 2862 rows containing missing values (geom_segment).
## Warning: Removed 2867 rows containing missing values (geom_segment).
## Warning: Removed 3012 rows containing missing values (geom_segment).
## Warning: Removed 2463 rows containing missing values (geom_segment).
## Warning: Removed 2841 rows containing missing values (geom_segment).
## Warning: Removed 2518 rows containing missing values (geom_segment).
## Warning: Removed 2746 rows containing missing values (geom_segment).
## Warning: Removed 2460 rows containing missing values (geom_segment).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 3210 rows containing missing values (geom_segment).
## Warning: Removed 2795 rows containing missing values (geom_segment).
## Warning: Removed 2862 rows containing missing values (geom_segment).
knitr::include_graphics(paste0(fig.path, "Plesne_DESeq2", ".png"))plot_combintions <- crossing(Site = c("Certovo", "Plesne"),
Oxygen = c("Oxic", "Anoxic"))
Labelled_ASVs <- map(seq(length(Ps_obj_SIP_noTime_l)), ~plot_otus_by_density(Ps_obj_SIP_noTime_l[[.x]],
ASV2plot = filter(DESeq_res_SIP_byTime_LFC_sig_df, Site == plot_combintions$Site[.x], Oxygen == plot_combintions$Oxygen[.x])))## Loading required package: ggpomological
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Warning in psmelt(.): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
map(seq(length(Ps_obj_SIP_noTime_l)),
~save_figure(paste0(fig.path, "Labelled_ASVs_", paste(plot_combintions[.x, ], collapse = "_")),
Labelled_ASVs[[.x]],
pwidth = 16,
pheight = 12,
dpi = 600))## [[1]]
## [1] "05_Diff_abund_figures/Labelled_ASVs_Certovo_Anoxic.svgz"
##
## [[2]]
## [1] "05_Diff_abund_figures/Labelled_ASVs_Certovo_Oxic.svgz"
##
## [[3]]
## [1] "05_Diff_abund_figures/Labelled_ASVs_Plesne_Anoxic.svgz"
##
## [[4]]
## [1] "05_Diff_abund_figures/Labelled_ASVs_Plesne_Oxic.svgz"
plots2display <- list.files(path = paste0(fig.path),
pattern = "^Labelled_ASVs_(.*).png$",
full.names = TRUE)
knitr::include_graphics(plots2display)